Hi,
During my installation of the latest version of sfepy from source (GitHub repo) in Windows, I ran the command to test the various modules. I found that one test had failed, the one for test_homogenization_perfusion.py. I ran the test in raise mode and the output is show below.
P.S.: I installed all of the optional dependencies except igakit, petsc4py, slepc4py, pymetis, scikits.umfpack and pysparse.
I hope this helps. Let me know if you need any other details.
Thanks.
Roshan Suresh Kumar
<<< directory: tests, test files: 1
<<< [1] tests\test_homogenization_perfusion.py
[1] sfepy: left over: ['__name__', '__doc__', '__package__', '__loader__', '__spec__', '__file__', '__cached__', '__builtins__', 'print_function', 'absolute_import', 'six', 'input_name', 'TestCommon', 'verbose', '_filename']
>>> test instance prepared (1 test(s))
run_tests.py:105: DeprecationWarning: time.clock has been deprecated in Python 3.3 and will be removed from Python 3.8: use time.perf_counter or time.process_time instead
tt = time.clock()
../examples/homogenization/perfusion_micro.py
[1] sfepy: left over: ['__name__', '__doc__', '__package__', '__loader__', '__spec__', '__file__', '__cached__', '__builtins__', 'absolute_import', 'match_x_plane', 'match_y_plane', 'cb', 'nm', 'data_dir', 'six', 'range', 'get_mats', 'recovery_perf', 'geoms', 'pb_def', 'eps0', 'param_h', 'aux', 'ch', 'val', 'all_periodicYM', 'all_periodicY', 'reg_io', 'ebcs_eta', 'ebcs_gamma', 'ch2', 'val2', 'aux_bY', 'i_io', 'io', 'ion', 'matk1', 'matk2', 'ipm', 'ireg', 'coefs', 'requirements', 'ipm2', 'get_channel', 'set_corrpis', 'set_corr_S', 'set_corr_cc', 'i_io2', 'io2', 'io12', 'verbose', '_filename']
homogen: reading mesh [line2, tri3, quad4, tetra4, hexa8] (C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\meshes\3d\perfusion_micro3d.mesh)...
homogen: ...done in 0.12 s
homogen: creating regions...
homogen: Y
homogen: YM
homogen: Pl
homogen: Pr
homogen: Pn
homogen: Pf
homogen: bYm
homogen: bYp
homogen: YA
homogen: fixedYA
homogen: YB
homogen: fixedYB
homogen: PlYM
homogen: PrYM
homogen: PnYM
homogen: PfYM
homogen: bYMA
homogen: PlYA
homogen: PrYA
homogen: PnYA
homogen: PfYA
homogen: bYA_1
homogen: bYA_2
homogen: bYA_3
homogen: bYMB
homogen: PlYB
homogen: PrYB
homogen: PnYB
homogen: PfYB
homogen: bYB_1
homogen: bYB_2
homogen: bYB_3
homogen: bYMp
homogen: bYMm
homogen: bYA
homogen: bYB
homogen: bYMpm
homogen: bYMchs
homogen: bYA_n1
homogen: bYA_n2
homogen: bYA_n3
homogen: bYB_n1
homogen: bYB_n2
homogen: bYB_n3
homogen: YMmchs
homogen: ...done in 0.25 s
homogen: using solvers:
ts: no ts
nls: newton
ls: ls
he: computing dependency corrs_gamma_m...
he: equation "eq_gamma_pm":
he: dw_diffusion.iV.YM(mat2M.k, qM, pM) =
1.000000e+00 * dw_surface_integrate.iS.bYMm(qM)
he: updating variables...
he: ...done
he: setting up dof connectivities...
he: ...done in 0.01 s
he: matrix shape: (1992, 1992)
he: assembling matrix graph...
he: ...done in 0.01 s
he: matrix structural nonzeros: 25154 (6.34e-03% fill)
he: updating materials...
he: mat2M
he: ...done in 0.03 s
he: using solvers:
ts: no ts
nls: newton
ls: ls
he: updating variables...
he: ...done
he: updating variables...
he: ...done
he: updating materials...
he: mat2M
he: ...done in 0.00 s
he: nls: iter: 0, residual: 6.480876e-02 (rel: 1.000000e+00)
he: residual: 0.04 [s]
he: matrix: 0.03 [s]
he: solve: 0.09 [s]
he: nls: iter: 1, residual: 3.816937e-16 (rel: 5.889539e-15)
he: solved in 1 steps in 0.38 seconds
he: ...done
he: computing Volume_total...
he: equation "tmp":
he: d_volume.iV.Y(vol_all)
he: updating materials...
he: ...done in 0.00 s
he: ...done
he: computing Volume_one...
he: ...done
he: computing Volume_bYMp...
he: equation "tmp":
he: d_surface.iS.bYMp(pM)
he: updating materials...
he: ...done in 0.00 s
he: ...done
he: computing Volume_bYp...
he: equation "tmp":
he: d_surface.iS.bYp(vol_all)
he: updating materials...
he: ...done in 0.00 s
he: ...done
he: computing Volume_bYMm...
he: equation "tmp":
he: d_surface.iS.bYMm(pM)
he: updating materials...
he: ...done in 0.00 s
he: ...done
he: computing Volume_bYm...
he: equation "tmp":
he: d_surface.iS.bYm(vol_all)
he: updating materials...
he: ...done in 0.00 s
he: ...done
he: computing Volume_bYA_1...
he: equation "tmp":
he: d_surface.iS.bYA_1(pA)
he: updating materials...
he: ...done in 0.00 s
he: ...done
he: computing Volume_bYA_2...
he: equation "tmp":
he: d_surface.iS.bYA_2(pA)
he: updating materials...
he: ...done in 0.00 s
he: ...done
he: computing Volume_bYA_3...
he: equation "tmp":
he: d_surface.iS.bYA_3(pA)
he: updating materials...
he: ...done in 0.00 s
he: ...done
he: computing Volume_bYB_1...
he: equation "tmp":
he: d_surface.iS.bYB_1(pB)
he: updating materials...
he: ...done in 0.00 s
he: ...done
he: computing Volume_bYB_2...
he: equation "tmp":
he: d_surface.iS.bYB_2(pB)
he: updating materials...
he: ...done in 0.00 s
he: ...done
he: computing Volume_bYB_3...
he: equation "tmp":
he: d_surface.iS.bYB_3(pB)
he: updating materials...
he: ...done in 0.00 s
he: ...done
he: computing Hmp...
he: equation "tmp":
he: ev_surface_integrate.iS.bYMp(corr_M)
he: updating materials...
he: ...done in 0.00 s
he: ...done
he: computing dependency corrs_gamma_p...
he: equation "eq_gamma_pm":
he: dw_diffusion.iV.YM(mat2M.k, qM, pM) =
1.000000e+00 * dw_surface_integrate.iS.bYMp(qM)
he: updating variables...
he: ...done
he: setting up dof connectivities...
he: ...done in 0.00 s
he: matrix shape: (1992, 1992)
he: assembling matrix graph...
he: ...done in 0.01 s
he: matrix structural nonzeros: 25154 (6.34e-03% fill)
he: updating materials...
he: mat2M
he: ...done in 0.03 s
he: using solvers:
ts: no ts
nls: newton
ls: ls
he: updating variables...
he: ...done
he: updating variables...
he: ...done
he: updating materials...
he: mat2M
he: ...done in 0.00 s
he: nls: iter: 0, residual: 7.140562e-02 (rel: 1.000000e+00)
he: residual: 0.01 [s]
he: matrix: 0.04 [s]
he: solve: 0.09 [s]
he: nls: iter: 1, residual: 3.887365e-16 (rel: 5.444059e-15)
he: solved in 1 steps in 0.37 seconds
he: ...done
he: computing Hpm...
he: equation "tmp":
he: ev_surface_integrate.iS.bYMm(corr_M)
he: updating materials...
he: ...done in 0.00 s
he: ...done
he: computing dependency corrs_etaA...
he: equation "eq_eta":
he: dw_diffusion.iV.YM(mat2M.k, qM, pM) = 0
he: updating variables...
he: ...done
he: setting up dof connectivities...
he: ...done in 0.00 s
he: matrix shape: (1992, 1992)
he: assembling matrix graph...
he: ...done in 0.01 s
he: matrix structural nonzeros: 25154 (6.34e-03% fill)
he: updating materials...
he: mat2M
he: ...done in 0.02 s
he: using solvers:
ts: no ts
nls: newton
ls: ls
he: updating variables...
he: ...done
he: updating variables...
he: ...done
he: updating materials...
he: mat2M
he: ...done in 0.00 s
he: nls: iter: 0, residual: 1.862908e-01 (rel: 1.000000e+00)
he: residual: 0.01 [s]
he: matrix: 0.03 [s]
he: solve: 0.09 [s]
he: nls: iter: 1, residual: 4.052551e-16 (rel: 2.175390e-15)
he: solved in 1 steps in 0.35 seconds
he: ...done
he: computing EmA...
he: equation "tmp":
he: ev_surface_integrate.iS.bYMm(corr_M)
he: updating materials...
he: ...done in 0.00 s
he: ...done
he: computing dependency corrs_gamma_B_1...
he: equation "eq_gamma":
he: dw_diffusion.iV.YB(mat2B.k, qB, pB)
+ dw_volume_dot.iV.YB(qB, lsB)
= 1.000000e+00 * dw_surface_integrate.iS.bYB_1(qB)
he: equation "eq_imv":
he: dw_volume_dot.iV.YB(lvB, pB) = 0
he: updating variables...
he: ...done
he: setting up dof connectivities...
he: ...done in 0.00 s
he: lcbc: imvB
he: dofs: total 1406, free 694, constrained 712, new 1
he: -> active 695
he: matrix shape: (1406, 1406)
he: assembling matrix graph...
he: ...done in 0.01 s
he: matrix structural nonzeros: 22052 (1.12e-02% fill)
he: updating materials...
he: mat2B
he: ...done in 0.01 s
he: using solvers:
ts: no ts
nls: newton
ls: ls
he: updating variables...
he: ...done
he: lcbc: imvB
he: dofs: total 1406, free 694, constrained 712, new 1
he: -> active 695
he: updating variables...
he: ...done
he: lcbc: imvB
he: dofs: total 1406, free 694, constrained 712, new 1
he: -> active 695
he: updating materials...
he: mat2B
he: ...done in 0.00 s
he: nls: iter: 0, residual: 9.945233e-03 (rel: 1.000000e+00)
he: residual: 0.01 [s]
he: matrix: 0.01 [s]
he: solve: 0.01 [s]
he: nls: iter: 1, residual: 2.133885e-16 (rel: 2.145636e-14)
he: solved in 1 steps in 0.13 seconds
he: ...done
he: computing RB_2_1...
he: equation "tmp":
he: ev_surface_integrate.iS.bYB_2(corr1_B)
he: updating materials...
he: ...done in 0.00 s
he: ...done
he: computing dependency corrs_oneB...
he: ...done
he: computing dependency corrs_etaB...
he: equation "eq_eta":
he: dw_diffusion.iV.YM(mat2M.k, qM, pM) = 0
>>> <class 'ValueError'>
Traceback (most recent call last):
File "run_tests.py", line 234, in <module>
sys.exit(main())
File "run_tests.py", line 223, in main
run_tests(stats, dirname, [filename])
File "run_tests.py", line 144, in run_tests
stats[0] + 1)
File "run_tests.py", line 108, in run_test
ifile=ifile)
File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\base\testing.py", line 67, in run
ret = test_method()
File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\tests\test_homogenization_perfusion.py", line 51, in test_solution
coefs = app()
File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\applications\application.py", line 29, in call_basic
return self.call(**kwargs)
File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\homogen_app.py", line 174, in call
aux = self.he(ret_all=ret_all, time_tag=time_tag)
File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\applications\application.py", line 29, in call_basic
return self.call(**kwargs)
File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\engine.py", line 729, in call
self.app_options.store_micro_idxs, time_tag)
File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\engine.py", line 107, in __call__
time_tag)
File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\engine.py", line 281, in calculate_req
chunk_tab, 'reqs', proc_id)
File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\engine.py", line 149, in calculate
val = mini_app(data=data)
File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\homogenization\coefs_base.py", line 459, in __call__
problem.set_equations(self.equations)
File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\discrete\problem.py", line 525, in set_equations
user=user)
File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\discrete\equations.py", line 66, in from_conf
materials, integrals, user=user)
File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\discrete\equations.py", line 772, in from_desc
terms.assign_args(variables, materials, user)
File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\terms\terms.py", line 299, in assign_args
term.assign_args(variables, materials, user)
File "C:\Users\rosha\Desktop\SEAK Lab\KDDDMM\sfepy-master\sfepy\terms\terms.py", line 512, in assign_args
raise ValueError('argument %s not found!' % arg_name)
ValueError: argument qM not found!
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